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install rosetta problems

Hi,
I am trying install rosetta on the fedora system,with gcc 4.1.2 and scons 2.0.1. But I encountered a problem while I install with the command:scons bin mode=release.
there are two warnings that always repeat again and again, I do not know how to solve this problem.
scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/xtal_programs/rosetta3.2.1/rosetta_source/SConscript", line 40, in

scons: warning: No hashlib or MD5 module available, CacheDir() not supported

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Pyrosetta 2.0 - Dunbrak library binary not loading - strange repacking score

All,

I am getting large energy increases when repacking a protein using v2.0 of PyRosetta.ScientificLinux64bit (I'm running RHEL5.5_64, Python 2.66)

1st issue On init(), I recieve:


basic.io.database: Database file opened: .../minirosetta_database/Rama_smooth_dyn.dat_ss_6.4
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 7533 residue types
core.pack.task: Packer task: initialize from command line()
Warning: Unable to locate database file Dunbrack02.lib.bin

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Generate structural fragments

Hello everyone,when I run "/rosetta/fragments/nnmake/make_fragments.pl -nopsipred -nosam -nojufo -noprof -verbose trhl2.fasta",I got the error follow:
[root@localhost input]# /rosetta/fragments/nnmake/make_fragments.pl -nopsipred -nosam -nojufo -noprof -verbose trhl2.fasta
Run options:
be verbose.
don't run psipred.
don't run prof.
don't run jufo.
don't run sam.
FILENAME: trhl2.fasta
no id specified. parse filename instead.
INTERMEDIATE: trhl2.fasta
ID: trhl CHAIN: 2
Warning: can't find executable file /work/chu/src/shareware/psipred/bin/psipred!

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abinitio - is there a way to limit number of CPU cores the program uses?

So the lab I'm working in has access to a 16 core server but we were told to use no more than 8 cores for any one application. So I was wondering if there is a way to limit the number of cores that abinitio uses while it runs its folding simulations? I looked through the help but didn't see anything that looked like it was what I'm looking for. Thanks for the help.

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Pyrosetta energy function

I am considering various conformations of a given protein and I should compare their corresponding energy values. I have used Pyrosetta to compute the energies using the "scorefxn = create_score_function('standard')" command. I was under the impression that the PDB structure of a protein should have the minimum energy.

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'DockingProtocol' object has no attribute 'setup_foldtree'

Hi around, sorry for disturbing with my problem that I haven't found posted or solved and if it has been solved I didn't find it. I recently downloaded PyRosetta and would like to use it for docking. The easiest, I thought, is to take an example script that comes with PyRosetta - docking.py, taking the test_dock.pdb that also comes with PyRsoetta and run it to get an idea about computational time. But it doesn't work by writing:
=========
docking.py in ()
15 print "setting up docking fold tree"

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Problem readin .ccp4 map file

Hi all,
I have bin trying to run the electron_density/molecular_replacement demo at step 4 run_rosetta_mr_nogap.sh and I get the following error. There is nothing wrong with the ccp4 map file (opens fine in other programs)but it appears to be looking for a MRC format map. How do I get the program to accept the ccp4 map?

core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ ERROR ] Error opening MRC map MR.1_2mFo-DFc.ccp4. Not loading map.

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